Organ‐based clues for diagnosis of inborn errors of immunity: A practical guide for clinicians

Abstract Inborn errors of immunity (IEI) comprise a group of about 490 genetic disorders that lead to aberrant functioning or the development of distinct immune system components. So far, a broad spectrum of IEI‐related manifestations has been noted in the literature. Due to overlapping signs and symptoms of IEI, physicians face challenges in appropriately diagnosing and managing affected individuals. The last decade has witnesses improving in the molecular diagnosis of IEI patients. As a result, it can be the mainstay of diagnostic algorithms, prognosis, and possibly therapeutic interventions in patients with IEI. Furthermore, reviewing IEI clinical complications demonstrates that the manifestations and severity of the symptoms depend on the involved gene that causes the disease and its penetrance. Although several diagnostic criteria have been used for IEI, not every patient can be explored in the same way. As a result of the failure to consider IEI diagnosis and the variety of diagnostic capabilities and laboratory facilities in different regions, undiagnosed patients are increasing. On the other hand, early diagnosis is an almost essential element in improving the quality of life in IEI patients. Since there is no appropriate guideline for IEI diagnosis in different organs, focusing on the clues in the patient's chief complaint and physical exams can help physicians narrow their differential diagnosis. This article aims to provide a practical guide for IEI diagnosis based on the involved organ. We hope to assist clinicians in keeping IEI diagnosis in mind and minimizing possible related complications due to delayed diagnosis.


| INTRODUCTION
Immune system defects constitute two major categories: primary (inherited) and secondary (acquired). Primary immunodeficiency, or inborn errors of immunity (IEI), predisposes individuals to an increased susceptibility to various combinations of recurrent infections, malignancy, autoimmunity, atopy, and lymphoproliferation. 1 These inherited disorders influence both the humoral and cellular arms of the immune system. Up to now, about 490 IEI have been identified that affect different innate and adaptive immune system components. 2 Many of them remain without a molecular diagnosis. 3 Regarding the involved organ and the underlying pathophysiology, the clinical picture of IEI is highly variable. Clinical presentations can range from asymptomatic (identified by newborn screening or family genetic test) to severe immunological defects and sometimes manifestations in nonimmune organs. 4,5 Patients are often underdiagnosed because of overlapping signs and symptoms with a high degree of incomplete penetrance, pleiotropy, and epistasis due to different IEI genetic defects. Moreover, many cases with severe forms of the disorder may die due to complications before being assessed. So, the exact prevalence of IEI is still unclear. Since improper management significantly impacts the mortality rate of patients with IEI, the most critical step by a physician is a timely diagnosis of a susceptible patient, mainly in settings without IEI newborn screening. Suspicion toward immunodeficiency in the differential diagnosis results from awareness of the unspecific symptoms. Therefore, it is recommended that almost all general practitioners and specialists continue their recognition of IEI phenotypes and diagnostic guidelines. 1 This article reviews common manifestations of IEI in different organs that guide the clinicians' suspicion toward immunodeficiency (Table 1).
consider PCD, TAP deficiency, and CF. 17,44 Chronic rhinosinusitis is a feature of complement deficiency, XLA, SIgAD, PCD, CF, HIES, DGS, CVID, and SAD. 17,20,21,32 SCID and AT predispose the patient to recurrent sinusitis. 21 Allergic rhinitis is reported in SIgMD. 10 Persistent rhinitis and chronic inflammation of the nares are noted in patients with CGD. 21,35 Chronic rhinitis is detected in infants with DGS. 35

| Common
Conjunctivitis can be a potent clue for the diagnosis of PAD. 45 Conjunctivitis is observed in SIgAD, SIgMD, WAS, autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED), and LAD type I. Bacterial conjunctivitis and keratoconjunctivitis caused by Hemophilus influenzae and Chlamydia trachomatis are specifically suggestive of XLA. Blepharokerato conjunctivitis is detected in CGD. Corneal scarring, secondary to conjunctivitis, is known as a complication of CGD, WAS, APECED, and XLA. Ophthalmologists who encounter patients suffering from bilateral keratitis should be aware of APECED. Ulcerative keratitis may suggest CGD and WAS. 10 Macular edema and uveitis are characteristic of CGD. Uveitis is reported in Blau syndrome, CVID, and mevalonate kinase deficiency (MKD). If recurrent hordeola secondary to Staphylococcus aureus and blepharitis are detected in a patient, SIgMD is among the first in the differential diagnosis list. 10

| Uncommon
Vitreous hemorrhage is seen in CGD or CVID. 1 5 | HEMATOLOGIC AND ONCOLOGICAL

| Uncommon
Medulloblastoma qualifies patients for further consideration of Bloom syndrome and NBS. 56 NBS can also evolve into dysgerminoma, glioma, and meningioma, while Bloom syndrome can predispose individuals to osteosarcoma. Neuroblastoma and thyroid cancer should alert physicians to NBS, AT, and DGS. 18,21,56 Patients with AT have a predisposition to parotid cancer. 21 Wilms tumor is seen in Bloom syndrome and DGS. Furthermore, clinicians should be alert for DGS when patients have hepatoblastoma, ALL, or teratoid/rhabdoid tumors. 56 Kaposi sarcoma is seen in OX40 deficiency. 14 Congenital asplenia is reported in isolated congenital asplenia. Thymoma is described as a feature of Good Syndrome. 14 Absent or hypoplastic thymus and abnormal thymic epithelium on chest X-ray or computed tomography could guide physicians to consider SCID, DGS, AT, defects of antigen presentation, PAX1 deficiency, and Winged helix deficiency. 1,21,62 6 | DERMATOLOGIC

| Common
Gastroesophageal reflux is mentioned in DGS, Bloom syndrome, and STAT3-HIES. Esophageal dysmotility and severe dysphagia are characteristic of STAT3-HIES and DGS, respectively. 18,33,74 Gastric diseases, including corpus-predominant autoimmune gastritis, autoimmune pan-gastritis, and lymphocytic gastritis, are detected in CVID and APECED. 5 The liver undergoes many changes in CVID, including abnormal liver biochemistries, primarily increased levels of alkaline phosphatase (ALP), nodular regenerative hyperplasia (NRH), and liver cirrhosis. 75 XLA and APDS can also predispose the patient to NRH. 76,77 A diagnosis of sclerosing cholangitis and cirrhosis by a gastroenterologist may suggest the presence of CD40 ligand deficiency. 1 Hepatitis is reported in APDS, APECED, IPEX, X-linked HIGM, STAT1 GOF, and STAT3 GOF. 6,16 CHH and CGD can exhibit hepatosplenomegaly. Moreover, splenomegaly is detected in CVID, ALPS, hypereosinophilia, and CHH. 6,9,16,35,65 Constipation is a common complication among patients with DGS. 33 Diarrhea accompanied by constipation, abdominal pain, and failure to thrive can be developed in 32%-48% of patients with CGD. Recurrent diarrhea is a characteristic of XLA, SCID, defects of antigen presentation, and CHH. 5,9,21 Watery diarrhea is seen in CVID. 5 Patients with SDS can present with steatorrhea. 50 Inflammatory bowel disease (IBD) is a clinical diagnosis that often brings patients with WAS, CVID, X-linked inhibitor of apoptosis (XIAP) deficiency, NEMO deficiency, CGD, or XLA to medical centers. 6,26,78 Colitis is a clinical finding in CVID, dominant-negative defects in CARD11, and CGD. 6 CVID and SIgAD could simulate celiac disease. CVID can also cause patchy chronic active enterocolitis accompanied by lymphoid hyperplasia and granulomata, which resemble Crohn's disease. 5 G. lamblia is recognized as the leading cause of gastroenteritis in CVID. 79 Giardiasis and strongyloidiasis are detected in SIgAD. Patients with XLA may also suffer from chronic giardiasis. 5

| Uncommon
DGS can rarely develop laryngeal web, esophageal atresia, and tracheoesophageal fistula. 33 The pyogenic liver abscess is diagnosed in PLS and CGD. 10,80 Venoocclusive disease with immunodeficiency (VODI) syndrome can be associated with hepatomegaly and venoocclusive disease. 14 Investigation of exocrine pancreatic insufficiency and malabsorption may provide a guide to diagnosing SDS. 1 GI-related lymphoid hyperplasia is found in APDS. 6 Autoimmune enteropathy is seen in CHH, CTLA-4 haploinsufficiency and deficiency of LRBA, IPEX, and STAT3 GOF. 5,9 STAT3-HIES has an increased susceptibility to spontaneous intestinal perforations and less likely fungal infections of the GI tract (typically histoplasmosis, Cryptococcus, and Coccidioides). 74 Intestinal dysfunction is detected in APECED. 6 Intestinal malrotation, Hirschsprung disease, imperforate anus, and the umbilical, inguinal, and diaphragmatic hernia may serve as a hint to identify DGS. 33 Intestinal obstruction and vomiting are identified in immunodeficiency with multiple intestinal atresia. 81 Early-onset enteric fistula is reported in IL10, IL10RA, and IL10RB deficiencies. 14

| ENDOCRINE
Hashimoto's thyroiditis is diagnosed in patients with IPEX. Autoimmune thyroiditis is associated with milder forms of ADA deficiency. In general, thyroid disease should be taken into consideration in patients with STAT1 GOF and Schimke immuno-osseous dysplasia (SIOD). 6,10,82 Hypo-or hyperthyroidism is investigated in CHH and rarely DGS. 9,33 SIgAD, IPEX, and WAS are the three main thyroiditis-associated IEI. 4 Hypoparathyroidism and consequent hypocalcemia are the most common endocrinopathy in DGS, chromosome 10p13-p14 deletion syndrome (10p13-p14DS), APECED, CMC, CHH, and CVID. 4,9,21,83 Osteoporosis compromises the quality of life in patients with CVID. 47,84 The risk of type 1 diabetes (T1D) is higher in patients with IPEX (FOXP3, forkhead box P3), WHIM syndrome, autoimmune polyglandular syndrome type 1 (APS type 1 due to AIRE mutation), CTLA4 mutation, deficiency of LRBA, milder forms of ADA deficiency, and STAT1 GOF. It should not be overlooked to assess intensive genetic analysis, including IEI-related genes in a patient whose onset of T1D is before six months of age. 4,6 Type 2 diabetes (T2D) development is noticed in AT. 82 Generally, AT, CF, IEI with DNA repair impairments, and Bloom syndrome can have an association with diabetes mellitus. 4,85 Adrenal insufficiency due to the autoimmune inflammation is probable in the nuclear factor kappa B (NF-κB) transcription factors dysfunction, mutations in MCM4, AIRE, or CTLA4, and DAVID syndrome (CVID accompanied by adrenocorticotropic hormone (ACTH) insufficiency). Meanwhile, adrenal insufficiency due to adrenal hypoplasia is associated with MIRAGE (myelodysplasia, infection, restriction of growth, adrenal hypoplasia, genital phenotypes, and enteropathy) syndrome due to SAMD9/SAMD9L gene mutations. 4

| REPRODUCTIVE SYSTEM AND THE UROLOGICAL
An absent uterus is investigated in DGS. 33 Premature ovarian failure develops in APECED and CVID. 4,86 A diagnosis of ovarian insufficiency with severe neutropenia may indicate Kostmann disease due to HAX1 gene mutations. 4 Pubertal delay is seen in AT. 18 Early menopause is reported in Bloom syndrome. 18 Bloom syndrome, CF, and CHH can predispose the patient to infertility. 14,85 Micropenis and the absence of pubertal development are observed in CHARGE syndrome (Heterozygous CHD7 gene deficiency). 4 Cryptorchidism, together with hypospadias, is reported in DGS. Individuals with Kabuki Syndrome could develop urinary tract malformation and premature thelarche. 33 Urogenital malformation is also reported in GATA2 deficiency. 87

| RENAL
Glomerulonephritis is observed in APDS. 6 Lupus-like glomerulonephritis can be formed in deficiency of early components of the classical complement pathway. 16 Membranoproliferative glomerulonephritis type 2 (MPGN2) and atypical hemolytic-uremic syndrome (HUS) should raise suspicion toward complement factor H deficiency. 10 IgA nephropathy is seen in WAS. 90 Progressive renal failure can occur in SIOD. 10 Renal anomalies/agenesis and hydronephrosis are identified in DGS. 33 Granuloma of the kidneys is reported in Blau syndrome. 10 Vesico-renal-genital anomaly is manifested in CHARGE syndrome, G6PC3 deficiency, and Malpuech, Michels, Mingarelli, and Carnevale (3MC) syndrome. 14

| CARDIAC
Interrupted aortic arch is noticed in DGS. 21 Aneurysms are indicated in all subtypes of HIES and STAT1 GOF (due to heterozygous variants in the STAT1 gene). 6,32 Pseudoaneurysms, congenital patent ductus venosus, superior vena cava syndrome, vasculitides, vascular ectasia, and thrombosis are noted in all subtypes of HIES. 32 Patients with STAT3-mutated HIES may be visited by a cardiologist due to coronary artery tortuosity or dilation. 32 Venous angeictasis is revealed in G6PC3 deficiency. 14 Angioedema is reported in C1 inhibitor and factor XII deficiencies. 14 The finding of peak systolic aortic pressure in high cutoff levels and mild valvular regurgitation in patients with CVID highlights the need for regular cardiac monitoring to control the sequels such as pulmonary arterial hypertension. 91 Murmur or cyanosis suggestive of congenital heart defects (particularly conotruncal anomalies) is associated with DGS, severe congenital neutropenia (SCN) type 4, CHARGE syndrome, Kabuki Syndrome, and MST1/STK4 deficiency. 10,16,33 G6PC3 deficiency could be characterized by a congenital heart disorder. 14 Pericarditis is a cardiac finding in patients with APDS. 6 IFNAR1 deficiency could predispose the patient to multisystem inflammatory syndrome (MISC) after coronavirus disease (COVID-19). 92 Individuals with DGS are at high risk of developing palatal abnormalities like velopharyngeal incompetence, overt cleft palate, cleft lip with or without cleft palate, and Pierre Robin, as well as subtle dysmorphic features. 33 A distinctive facial appearance along with a high and prominent forehead, prognathism or retrognathism, enlargement of the interalar distance, thickening of the soft tissues of the ear or nose, and the high arched palate can be suggestive of HIES. 32,93 A rough skin appearance with exaggerated pore size is mentioned in HIES with STAT3 mutation. This characteristic appearance becomes evident with age. 94 It is suggested that suspicions of HIES with PGM3 mutations should increase when wide nostrils and prominent lips develop. 32 NBS is characterized by a bird-like face. 10 In conclusion, if facial abnormalities are observed in a neonate, DGS, ICF syndrome, 3MC syndrome type 2 (COLEC11 deficiency), Cohen syndrome (COH1 deficiency), ITCH deficiency, STAT5B deficiency, FILS (facial dysmorphism, immunodeficiency, livedo, and short stature) syndrome, RNF168 deficiency, Kabuki Syndrome, Cernunnos (XLF), and Bloom syndrome are among the first in the differential diagnosis list. 10,95 14 | ODONATOLOGICAL Retention of deciduous teeth is one of the clinical findings in HIES. A delay in the shedding of primary teeth is seen in STAT3 deficiency. 1,93 Patients' dental enamel hypoplasia may suggest an onset of APECED or DGS. 1,33 Gingivitis is manifested in neutrophil deficiency or CGD. 16,17 Intermittent stomatitis is reported in HIGM and cyclic neutropenia. 17,35,96 Ulcerative stomatitis is noted in CGD. 35 Severe periodontitis and, consequently, premature loss of teeth are reported in CHD, LAD type I, and PLS. 10,17

| PSYCHIATRIC AND INTELLECTUAL CHARACTERISTICS
Several neurocognitive disorders among patients with DGS are reported, including motor delays (often with hypotonia) and speech/language deficits (in infancy), and learning difficulties (in childhood). 33 Cognitive impairment coinciding with a neurological defect and a myelodysplastic syndrome should alert physicians to Kostmann disease (HAX1 gene mutation). 1 AT and syndromic CIDs can predispose individuals to cognitive defects. 14,55 Developmental delay is indicated in 3MC syndrome, LAD type 2, Cohen syndrome, Kabuki syndrome, Barth syndrome, P14 deficiency, adenosine deaminase acting on RNA 1 (ADAR1) deficiency, HIES with PGM3 mutations, PNP deficiency, MKD, DGS, NBS, and ITCH deficiency. 10,32 Mild to moderate intellectual disability is seen in DGS, b-actin deficiency, HIES with PGM3 mutations, Kabuki Syndrome, Bloom syndrome, NBS, CHD, and ICF syndrome. 10,17,18,32,33 A variety of psychiatric disorders like attention deficit with hyperactivity disorder (ADHD), autism spectrum disorder (ASD), anxiety, mood disorders, and schizophrenia can be associated with DGS. 33 16 | NEUROLOGICAL

| Common
Meningitis is reported in PAD, XLA, WAS, HIES with DOCK8-deficiency, and complement deficiency. 21,32,45,97 Chronic enteroviral meningoencephalitis is revealed in XLA. 45 Encephalopathy and encephalomyelitis are seen in CVID. 98 Viral encephalitis could be a clinical feature of TLR3, UNC93B1, TRAF3, TRIF, TBK1 deficiencies. 14 Hypo-calcemic seizures are one of the presentations of DGS. 1 Seizure is seen in Kabuki syndrome. 10 An association between peripheral neuropathy or myelopathy and CVID has been documented previously. 98 Peripheral neuropathy is also reported in CHD. 17 Cranial neuropathy is detected in Blau Syndrome. 10 Multifocal motor axonal neuropathy and narcolepsy guide neurologists to consider CHH. 9 Fibromyalgia is noted in IgGSD. 99 Aneurysms often found incidentally in brain imaging are highly suggestive of STAT3-mutated HIES. 1 Brain infarction is indicative for HIES with DOCK8-deficiency. 32 Patients with ADA2 deficiency can manifest increased susceptibility to CNS involvement in the form of ischemic or hemorrhagic strokes. 68 Central nervous system (CNS) vasculitis is noticed in XLP. 49 Spontaneous CNS candidiasis is reported in CARD9 deficiency. 100

| Common
Fractures following minor trauma, scoliosis, osteoporosis, degenerative spine disease, craniosynostosis, or hyperextensive joints can suggest a HIES diagnosis. Scoliosis, craniosynostosis, and cervical and thoracic vertebral anomalies are seen in DGS. 1,32,33,93 Scoliosis is demonstrated in HIES with PGM3 mutations and Kabuki syndrome. 10,32 Bone and joint infections such as Mycoplasma arthritis are detected in CVID or XLA. 45 Osteomyelitis is noted in CGD and XLA. 35 DIRA (deficiency of the interleukin 1 receptor antagonist) syndrome secondary to defects in IL1RN might develop neonatal sterile multifocal osteomyelitis. 1 Severe fungal osteomyelitis of the skull base is a rare manifestation of myeloperoxidase (MPO) deficiency. 17

| Uncommon
Dystrophy is reported in the CANDLE (Chronic Atypical Neutrophilic Dermatosis with Lipodystrophy and Elevated temperature) syndrome. Chondrodysplasia and short stature might occur in SDS, while skeletal dysplasia, short stature, and limb dwarfism are mentioned in RNF168, MCM4, ACTB, ACP5, STAT5B, FILS, SMARCAL1, RMPR, and BLM gene mutations. 1,50 Costochondral junction flaring is identified in ADA deficiency. 1 If the physician encounters a patient with spondylo-epiphyseal dysplasia, then SIOD should be ruled out. 10 Finger and spinal deformities, slipped capital femoral epiphysis, and rib cage abnormalities are reported in SDS. 50 Hip dislocation is a clinical feature of Kabuki syndrome. 10 Camptodactyly is illustrated in Blau syndrome, whereas DGS can rarely develop clubfoot and polydactyly. 10,33 18 | OTHER Disseminated lymphadenopathy is explored in CVID, Omenn syndrome, ALPS, or autosomal recessive HIGM. 16 Nonmalignant lymphadenopathy is marked in ALPS. 6 Cervical lymphadenopathy is noted in WAS, interferon-gamma (IFN-gamma)/interleukin-12 (IL-12) pathway defects, and CGD. 21,35 Lymphadenitis is described in HIES and cyclic neutropenia. 35,64 Absent lymph nodes are detected in XLA or SCID. XLA cases are at high risk of developing the absence of tonsils. 16 The mycobacterial abscess is reported in IFN-gamma/IL-12 pathway defects. 21 Disseminated infectious mononucleosis is reported in XLP. 21 Vaccine-associated poliomyelitis can occur in XLA. 21 CVID and SCID are associated with paralysis or diarrhea after taking the poliovirus vaccine. 14 Suspicions of CMC should increase when white adherent plaques of thrush or angular cheilitis (or perlèche) are detected. 17 Leukoplakia of the oral mucosa is manifested in DKC. 10 Epistaxis and oral bleeding are seen in WAS. 65 Patients with WAS show a predisposition to prolonged bleeding after circumcision. 21 X-linked DKC, Schimke syndrome, and syndromic diarrhea/tricho-hepato-enteric syndrome (SD/THE) are characterized by Intrauterine growth retardation. 14,101 Intrauterine polyhydramnios is reported in immunodeficiency with multiple intestinal atresia. 14 THI can be associated with prematurely born. 21 Delayed separation of the umbilical cord is the clinical hallmark of LADs and Rac2 deficiency. 14 Coarse face is presented in autosomal dominant HIES. 14 NEMO, STIM1, and ORAI1 deficiencies could be characterized by anhidrotic ectodermal dysplasia. 14 Hyponatremic dehydration is a clinical feature of CF. 85 Hypertension due to atypical hemolytic uremic is diagnosed in CD46, factor B, factor I, factor H, factor H-related protein, and thrombomodulin deficiencies. 14 High fever indicates the probability of NOMID. Recurrent febrile attacks should alert physicians toward MKD and familial Mediterranean fever. 10,102 Associated sarcoid-like granulomatous disease is detected in AT, SCID, and CVID. 103,104 Secondary amyloidosis is manifested in NOMID. 10

| CONCLUSION
Recently, many advances have emerged in the realms of both diagnosis and treatment aspects of IEI. 2 Since heterogeneous presentations of IEI pose diagnostic challenges for physicians, shedding light on the organ's involvement in IEI is an ever-important issue. In this review, we studied the manifestations of IEI in each part of the body as a whole to provide meaningful insights regarding the physician's clinical decision. Sometimes, characteristic features of organs such as the ear, blood, or skin could prompt the physician to consider IEI among the first in the differential diagnosis list. Meanwhile, due to the potential involvement of the lung, GI tract, and endocrine glands, awareness of their associated symptoms has contributed to greater comprehension of the following sequels. The current review shows that several manifestations of IEI can be misinterpreted as separate diseases and cause mismanagement.
Based on the previously published literature, many presentations are not routinely expected in patients with IEI. Accordingly, articles and tables containing all the symptoms reported in various types of IEI can provide a practical guide to the treating physician and specialists to define a proper diagnostic strategy and therapeutic protocols. The national and continent-based cohorts and different geographical reports of diagnostic signs and symptoms in various clinical or genetic forms of IEI are required for further advances. However, it is essential to mention that improved registration efforts and maintenance of the available databases are necessary to conduct future studies.
Regarding the increasing knowledge of IEI-associated disorders, the latter concern applies to developing targeted diagnostic guidelines for clinicians based on their specialty. It is to be hoped that further elucidation of the related manifestations will ere long have implications for increasing the life expectancy of the patients suffering from IEI.

ACKNOWLEDGMENTS
We would like to express our gratitude and respect to professor Asghar Aghamohammadi, who, although no longer with us, continues to inspire by his example and dedication to the students he served over the course of his career.